I'm trying to reproduce the step 2 of AMBER A1 tutorial with VMD. (http://ambermd.org/tutorials/advanced/tutorial1/section2.htm) because Sirius is no longer available. However VMD can never
superposition the "anchor atoms" and the two structures (linker and dye) cannot be aligned as shown in the tutorial. I tried to increase the number of anchor atoms and the problem still exists. The
script is as